The government is facing questions over transparency after almost £2 million in aid and defence funding was given to security projects in Egypt, including support for policing, the criminal justice system and the treatment of juvenile detainees.

The news comes with Egypt’s security forces under fire from human rights groups for routine disappearances, the torture of detainees, and the jailing of political opponents and journalists.

Documents obtained under the Freedom of Information Act reveal the cash was granted to the Egyptian authorities through the conflict, stability and security fund (CSSF), the operations, objectives and achievement of which were described as “opaque” by a parliamentary inquiry earlier this year.

MPs and Lords criticised the secrecy of the £1.1bn fund, claiming they could neither scrutinise it nor provide taxpayers with information about how it was spent. The avowed aim of the secretive CSSF, which is financed by the aid and defence budgets, is to build security and tackle conflict overseas.

Human rights group Reprieve said it was concerned that £650,000 of the £1.85m security funding granted through the CSSF in 2015-16 “appeared to involve direct engagement with the Egyptian police and criminal justice system”, including programmes relating to juvenile detainees. Reprieve asked for further details from the Foreign and Commonwealth Office, but the request was refused on the grounds that it was not in the public interest.

Foa said: “Ministers are well aware of rights abuses by Egyptian courts and prisons, including against juveniles like Ibrahim Halawa. It is, therefore, deeply disturbing that the government refuses to release any information about its work with these serial human rights violators.

“Transparency in the use of taxpayer money is crucial where there is a risk that the UK could be contributing to abuses as serious as torture and illegal executions. The Foreign Office should urgently explain what these projects involve, and demonstrate they are not exacerbating the terrible ordeals of people like Ibrahim.”

The case of Halawa, an Irish citizen who has been detained in Egypt for five years awaiting trial, provides a stark reminder of the nature of criminal justice in Egypt under President Abdel Fatah al-Sisi.

Halawa, who faces the death penalty if convicted, was arrested with his three sisters during a protest against the ousting of Mohamed Morsi at a Cairo mosque in 2013. He was then 17, and a juvenile under international law. His sisters were released but he was charged, along with 493 others, with attending an illegal protest.

Intense diplomatic efforts by the Irish government have failed to secure Halawa’s release and his trial has been delayed more than 30 times, partly due to the complications inherent in organising a mass trial involving almost 500 defendants. Last year, he told the Guardian he had been stripped, beaten and left for dead after a hunger strike. On 29 June, Halawa’s case was postponed again, to 2 October, according to the FCO.

In a letter sent to Reprieve in response to its request for further information about the CSSF’s support for security initiatives in Egypt, the FCO said that “providing further detail about the projects could jeopardise the trust and confidence in us by the Egyptian government and therefore our ability to both protect and promote UK interests in the future”.

The revelations expose wider concerns about the rising percentage of Britain’s £13bn aid budget being spent by ministries other than the Department for International Development, and the implications of such spending for public scrutiny. Some 36% of aid is spent through other departments who have direct responsibility for that portion of budget.

Kate Osamor, the shadow international development secretary, called for all government departments to publish aid-related data. Osamor said: “This alarming case raises yet more urgent questions about how the National Security Council is deploying the CSSF to spend aid money that should be earmarked to help the world’s poorest.

“The government needs to come clean on how they are spending aid money through other departments, and make sure these other departments quickly get themselves up to DfID’s level of aid transparency. In this day and age, every government department should be publishing data for all aid-financed programmes, and not hiding behind the excuse of national security. The NSC should publish their country strategies, open up the CSSF to scrutiny, and tell the public whether or not our aid is being spent on detaining juveniles.”

In a recent briefing, the FCO reported that the human rights situation in Egypt “continues to deteriorate” with reports of torture, police brutality and enforced disappearance.

In a statement, a spokesman for the FCO said: “The UK is committed to working with Egypt to support political and economic reform, and we encourage the Egyptian government to deliver on its international and domestic human rights commitments. But it is not good enough to merely criticise other countries from the sidelines. We have to work with Egypt to encourage change. All projects carried out by the UK government comply with the UK’s domestic and international human rights obligations.”